3OTH

Crystal Structure of CalG1, Calicheamicin Glycostyltransferase, TDP and calicheamicin alpha3I bound form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.301 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Complete set of glycosyltransferase structures in the calicheamicin biosynthetic pathway reveals the origin of regiospecificity.

Chang, A.Singh, S.Helmich, K.E.Goff, R.D.Bingman, C.A.Thorson, J.S.Phillips, G.N.

(2011) Proc.Natl.Acad.Sci.USA 108: 17649-17654

  • DOI: 10.1073/pnas.1108484108
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Glycosyltransferases are useful synthetic catalysts for generating natural products with sugar moieties. Although several natural product glycosyltransferase structures have been reported, design principles of glycosyltransferase engineering for the ...

    Glycosyltransferases are useful synthetic catalysts for generating natural products with sugar moieties. Although several natural product glycosyltransferase structures have been reported, design principles of glycosyltransferase engineering for the generation of glycodiversified natural products has fallen short of its promise, partly due to a lack of understanding of the relationship between structure and function. Here, we report structures of all four calicheamicin glycosyltransferases (CalG1, CalG2, CalG3, and CalG4), whose catalytic functions are clearly regiospecific. Comparison of these four structures reveals a conserved sugar donor binding motif and the principles of acceptor binding region reshaping. Among them, CalG2 possesses a unique catalytic motif for glycosylation of hydroxylamine. Multiple glycosyltransferase structures in a single natural product biosynthetic pathway are a valuable resource for understanding regiospecific reactions and substrate selectivities and will help future glycosyltransferase engineering.


    Organizational Affiliation

    Department of Biochemistry, University of Wisconsin, 433 Babcock Drive, Madison, WI 53706, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CalG1
A, B
412Micromonospora echinosporaMutation(s): 0 
Gene Names: calG1
Find proteins for Q8KNF2 (Micromonospora echinospora)
Go to UniProtKB:  Q8KNF2
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CLJ
Query on CLJ

Download SDF File 
Download CCD File 
A, B
Calicheamicin alpha3I
S-[(2R,3S,4S,6S)-6-[[(2R,3S,4S,5R,6R)-4,5-dihydroxy-6-[[(2S,5Z,9R,13E)-9-hydroxy-12-(methoxycarbonylamino)-13-(2-methylsulfanyldisulfanylethylidene)-11-oxo-2-bicyclo[7.3.1]trideca-1(12),5-dien-3,7-diynyl]oxy]-2-methyl-oxan-3-yl]amino]oxy-4-hydroxy-2-methyl-oxan-3-yl] 4-[(2S,3R,4R,5S,6S)-3,5-dihydroxy-4-methoxy-6-methyl-oxan-2-yl]oxy-5-iodo-2,3-dimethoxy-6-methyl-benzenecarbothioate
C47 H59 I N2 O19 S4
LOIKQPQFDFXTOY-GZWKDLOHSA-N
 Ligand Interaction
TYD
Query on TYD

Download SDF File 
Download CCD File 
A, B
THYMIDINE-5'-DIPHOSPHATE
C10 H16 N2 O11 P2
UJLXYODCHAELLY-XLPZGREQSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.301 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 45.809α = 90.00
b = 100.100β = 90.00
c = 169.881γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
DENZOdata reduction
HKL-2000data collection
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2010-12-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-11-02
    Type: Database references
  • Version 1.3: 2012-08-08
    Type: Structure summary
  • Version 1.4: 2017-11-08
    Type: Refinement description